Although small-scale fisheries (SSF) play an important socio-economic role in developing nations, overfishing seems to be increasing the risk of stock vulnerability. This study aims to quantify the pressure of SSF on fish stocks in Sunda Strait (Indonesia) using several biological indicators that are important in quantifying fishing pressure. Data on these indicators were collected monthly for three years (2012–2014) in one of the main fishing ports of the area. The results provide evidence that, although SSF would appear to be the most environmentally sustainable of all the fishing techniques being used today in the coastal waters of Indonesia, the impact of SSF fishing on juvenile fishes in certain areas such as the Sunda Strait must not be underestimated. The results also show the need to protect immature fish of species that are not only commercialised but are also important in subsistence fisheries. Although further studies are needed to assess the impact of SSF on fish stocks in the area, it is suggested management recommendations that include the implementation of marine-protected areas in nursery grounds and establishing minimum landing sizes well above the size-at-maturity for each species, are needed.